His research focuses on the mechanisms underlying the origin of novelty (how new processes and functions originate). Most of his work involves the use of high-throughput DNA sequencing methods to characterize microbes and then the use and development of computational methods to analyze this type of data. In particular, his computational work has focused on integrating evolutionary analysis with genome analysis—so-called phylogenomics.

Previously, he applied this phylogenomic approach to cultured organisms, such as those from extreme environments and those with key properties as they relate to evolution or global climate cycles. Currently he is using sequencing and phylogenomic methods mostly to study microbes directly in their natural habitats (i.e., without culturing). In particular he focuses on how communities of microbes interact with each other or with plant and animal hosts to create new functions. Dr. Eisen has also coordinated one of the largest microbial genome sequencing projects to date—the “Genomic Encyclopedia of Bacteria and Archaea” being done at the Department of Energy (DOE) Joint Genome Institute.

Prior to moving to UC Davis he was on the faculty of The Institute for Genomic Research (TIGR) in Rockville, Maryland and held an Adjunct Appointment in the Department of Biology at the Johns Hopkins University.

He earned his Ph.D. in 1998 in Biological Sciences from Stanford University, where he worked on the evolution of DNA repair processes in the lab of Philip C. Hanawalt. He earned his undergraduate degree in Biology from Harvard College in 1990.

Shorter Bio

Jonathan Eisen is a Full Professor at the University of California, Davis with appointments in the School of Medicine and the College of Biological Sciences.

Dr. Eisen is a pioneer in the study of microbial diversity, in particular in the development and use of high throughput laboratory and computational methods to study microbes by analyzing their genomes. He has co-authored more than 200 papers and a highly rated Evolution textbook.

Dr. Eisen’s research focuses on communities of microbes and how they provide new functions - to each other or to a host. His study systems have included boiling acid pools, surface ocean waters, agents of many diseases, and the microbial ecosystems found in and on plants and animals. He is also coordinating the largest microbial sequencing project to date – a Genomic Encyclopedia – being done at the DOE Joint Genome Institute where he holds an Adjunct Appointment. His overarching goal in all of his research is to create a “Field Guide to the Microbes” much as exists for birds and trees.

In addition to his research, Dr. Eisen is a vocal advocate for “open science” especially "open access" to scientific publications and is the Academic Editor-in-Chief of PLoS Biology. He is also an active and award-winning blogger and microblogger.

Prior to moving to UC Davis he was on the faculty of The Institute for Genomic Research in Rockville, Maryland and held an Adjunct Appointment at the Johns Hopkins University. He earned his Ph.D. in Biological Sciences from Stanford University and his undergraduate degree in Biology from Harvard College.

Even shorter

Jonathan Eisen is a Full Professor at the University of California, Davis with appointments in the School of Medicine and the College of Biological Sciences.

Dr. Eisen is a pioneer in the study of microbial diversity, in particular in the development and use of high throughput laboratory and computational methods to study microbes by analyzing their genomes. He has co-authored more than 200 papers and a highly rated Evolution textbook.

Dr. Eisen’s research focuses on communities of microbes and how they provide new functions - to each other or to a host. His study systems have included boiling acid pools, surface ocean waters, agents of many diseases, and the microbial ecosystems in and on plants and animals. He is also coordinating the largest microbial sequencing project to date – a Genomic Encyclopedia – being done at the DOE Joint Genome Institute where he holds an Adjunct Appointment. His overarching goal in his research is to create a “Field Guide to the Microbes” much as exists for birds or trees.

In addition to his research, Dr. Eisen is a vocal advocate for “open science” especially "open access" to scientific publications and is the Academic Editor-in-Chief of PLoS Biology. He is also an active and award-winning blogger and science communicator.

Prior to UC Davis he was on the faculty of The Institute for Genomic Research and held an Adjunct Appointment at the Johns Hopkins University. He earned a Ph.D. in Biological Sciences from Stanford University and an A.B. in Biology from Harvard College.